The thermal stability of the Cu₂ZnSnSe₄ (CZTSe) absorber and CdS buffer layers in SLG/Mo/CZTSe/CdS/i-ZnO/ITO devices is explored by performing a series of soft (∼200 °C) post deposition treatments (PDTs). A comprehensive analysis of a sample comprised by 56 individual devices by means of Raman and photoluminescence spectroscopies coupled with optoelectronic characterization is performed at different PDT steps. This allows isolating the effects of the PDT on the CZTSe absorber and CdS buffer layer separately and reveals clear evidences of: i) a degradation of the absorber due to Cu/Zn disorder that hinders device performance, and ii) an improvement of the buffer layer by the recrystallization of the CdS nanolayer that is the main responsible for the PDT-induced efficiency improvement. As such, it is concluded that CZTSe/CdS based PV devices present a low thermal stability under relatively low temperatures (in the 100–200 °C range), comparable to the temperatures employed at the final production stages of thin film PV devices or even during device operation, that leads to significant changes in solar cell performance and needs to be taken into consideration for the further development of the kesterite PV technology. These results are supported by a novel methodology for easily discerning between changes in Cu/Zn disorder and in point defects concentration in kesterites based on solely on Raman spectroscopy that is proposed in this work and developed through the analysis of a set of CZTSe powder samples with strong variation of the order parameter Q.